Processing microtome slides with GIMP and ImageJ

Roman M. Link

Introduction

This is a simplified short form of the BOT2 tutorial for the pre-processing and analysis of wood anatomical microtome slides based on GIMP and ImageJ which is meant for in-class use.

A list of useful GIMP shortcuts can be found here: (https://www.gimpusers.com/gimp/hotkeys).

Note that the term CODE in this document is a placeholder that has to be replaced by the unique ID of sample you are working with! In the screenshots in this example, the CODE is CRI_3_010.

Important note

All ImageJ results tables can be saved either in ‘Comma Separated Value’ (.csv) or whitespace/tabstop separated format (generated when saving with a .xls extension, but actually just a plain text format). In either case, the output is optimized for US/UK locales, which means that points are used as a decimal separator. In order to process these files on German systems without compatibility issues, it is important to make sure that the system-wide decimal separator is correctly set before starting the analysis.

In German Windows 10, the option to change the decimal separator is well hidden:

Start Menu ➜ Windows-System ➜ Systemsteuerung ➜ Zeit und Region ➜ Region ➜ Formate ➜ Weitere Einstellungen ➜ Dezimaltrennzeichen

To avoid data compatibility problems, make sure the decimal separator is set to “.”. In this case, you will want the grouping symbol (Symbol für Zifferngruppierung) to be a comma instead of the point symbol used in Germany.

If you do not want to change your system settings, you can alternatively export everything in a .csv format and use Excel’s Daten ➜ Text in Spalten menu to manually set field delimitor and decimal separator.

Preparation in GIMP

Analysis in ImageJ

Error inspection in GIMP

the simplified workflow in the next couple of screenshots was documented on a computer running Ubuntu Mate and a different version of GIMP, but should work just the same on Windows

Final steps